Starting phenix.real_space_refine on Sat Aug 3 17:27:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/08_2024/8wss_37823.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/08_2024/8wss_37823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/08_2024/8wss_37823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/08_2024/8wss_37823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/08_2024/8wss_37823.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wss_37823/08_2024/8wss_37823.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5624 2.51 5 N 1489 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8797 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1749 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2560 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1720 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 149 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "R" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.31, per 1000 atoms: 0.60 Number of scatterers: 8797 At special positions: 0 Unit cell: (86.52, 122.776, 131.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1617 8.00 N 1489 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.6 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.911A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.623A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.108A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.959A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.672A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.656A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.944A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 225 removed outlier: 3.761A pdb=" N ASP H 224 " --> pdb=" O GLU H 221 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL H 225 " --> pdb=" O ALA H 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 221 through 225' Processing helix chain 'R' and resid 111 through 138 Processing helix chain 'R' and resid 145 through 173 Proline residue: R 166 - end of helix Processing helix chain 'R' and resid 181 through 216 removed outlier: 3.806A pdb=" N THR R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU R 187 " --> pdb=" O THR R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 222 Processing helix chain 'R' and resid 224 through 250 removed outlier: 4.050A pdb=" N VAL R 228 " --> pdb=" O ARG R 224 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU R 231 " --> pdb=" O SER R 227 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 272 through 286 removed outlier: 4.262A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 303 Processing helix chain 'R' and resid 313 through 348 removed outlier: 3.675A pdb=" N CYS R 337 " --> pdb=" O VAL R 333 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP R 338 " --> pdb=" O PHE R 334 " (cutoff:3.500A) Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 349 through 351 No H-bonds generated for 'chain 'R' and resid 349 through 351' Processing helix chain 'R' and resid 357 through 384 Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 392 removed outlier: 3.677A pdb=" N VAL R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.887A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.642A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.556A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.536A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.965A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.798A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.482A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.580A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.659A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 147 through 149 removed outlier: 3.541A pdb=" N GLU H 247 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP H 177 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 161 Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AB6, first strand: chain 'R' and resid 253 through 254 433 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2812 1.34 - 1.46: 2220 1.46 - 1.58: 3854 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 8983 Sorted by residual: bond pdb=" N ARG L 11 " pdb=" CA ARG L 11 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.37e-02 5.33e+03 7.13e+00 bond pdb=" N MET R 165 " pdb=" CA MET R 165 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.04e-02 9.25e+03 5.24e+00 bond pdb=" N ASN R 194 " pdb=" CA ASN R 194 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.97e+00 bond pdb=" N SER R 195 " pdb=" CA SER R 195 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.90e+00 bond pdb=" N GLN R 196 " pdb=" CA GLN R 196 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.56e+00 ... (remaining 8978 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.94: 214 106.94 - 113.70: 4995 113.70 - 120.47: 3291 120.47 - 127.23: 3594 127.23 - 133.99: 95 Bond angle restraints: 12189 Sorted by residual: angle pdb=" CA GLY H 10 " pdb=" C GLY H 10 " pdb=" N LEU H 11 " ideal model delta sigma weight residual 114.23 116.73 -2.50 8.80e-01 1.29e+00 8.04e+00 angle pdb=" N THR R 272 " pdb=" CA THR R 272 " pdb=" C THR R 272 " ideal model delta sigma weight residual 113.18 109.75 3.43 1.33e+00 5.65e-01 6.63e+00 angle pdb=" O ASN R 194 " pdb=" C ASN R 194 " pdb=" N SER R 195 " ideal model delta sigma weight residual 122.12 124.64 -2.52 1.06e+00 8.90e-01 5.65e+00 angle pdb=" CA ASN R 194 " pdb=" C ASN R 194 " pdb=" O ASN R 194 " ideal model delta sigma weight residual 120.55 118.05 2.50 1.06e+00 8.90e-01 5.58e+00 angle pdb=" CA GLY H 10 " pdb=" C GLY H 10 " pdb=" O GLY H 10 " ideal model delta sigma weight residual 122.33 120.55 1.78 8.10e-01 1.52e+00 4.80e+00 ... (remaining 12184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.91: 4952 13.91 - 27.82: 242 27.82 - 41.74: 87 41.74 - 55.65: 21 55.65 - 69.56: 2 Dihedral angle restraints: 5304 sinusoidal: 1992 harmonic: 3312 Sorted by residual: dihedral pdb=" CA GLN R 196 " pdb=" CB GLN R 196 " pdb=" CG GLN R 196 " pdb=" CD GLN R 196 " ideal model delta sinusoidal sigma weight residual -180.00 -122.57 -57.43 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N LEU R 284 " pdb=" CA LEU R 284 " pdb=" CB LEU R 284 " pdb=" CG LEU R 284 " ideal model delta sinusoidal sigma weight residual -180.00 -125.25 -54.75 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CA LYS G 46 " pdb=" CB LYS G 46 " pdb=" CG LYS G 46 " pdb=" CD LYS G 46 " ideal model delta sinusoidal sigma weight residual -180.00 -125.41 -54.59 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 835 0.024 - 0.049: 318 0.049 - 0.073: 135 0.073 - 0.097: 66 0.097 - 0.121: 51 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA MET R 112 " pdb=" N MET R 112 " pdb=" C MET R 112 " pdb=" CB MET R 112 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO R 166 " pdb=" N PRO R 166 " pdb=" C PRO R 166 " pdb=" CB PRO R 166 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 1402 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 112 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO R 113 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 113 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 113 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 14 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO L 15 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO G 55 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.015 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 94 2.65 - 3.21: 7892 3.21 - 3.77: 13415 3.77 - 4.34: 18204 4.34 - 4.90: 30790 Nonbonded interactions: 70395 Sorted by model distance: nonbonded pdb=" OD1 ASP A 229 " pdb=" CD1 LEU A 232 " model vdw 2.082 3.460 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.220 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.239 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.241 3.040 nonbonded pdb=" NH1 ARG H 203 " pdb=" OD2 ASP H 224 " model vdw 2.254 3.120 ... (remaining 70390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.180 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8983 Z= 0.127 Angle : 0.456 6.082 12189 Z= 0.259 Chirality : 0.038 0.121 1405 Planarity : 0.003 0.049 1532 Dihedral : 9.953 69.560 3157 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.43 % Allowed : 8.53 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1119 helix: 2.57 (0.27), residues: 376 sheet: 1.50 (0.32), residues: 273 loop : -0.85 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 111 HIS 0.002 0.000 HIS R 179 PHE 0.007 0.001 PHE R 161 TYR 0.010 0.001 TYR R 275 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 244 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7345 (mtm110) REVERT: A 29 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7314 (ttpt) REVERT: A 195 HIS cc_start: 0.7562 (m-70) cc_final: 0.7216 (t70) REVERT: A 252 SER cc_start: 0.8985 (t) cc_final: 0.8691 (m) REVERT: B 79 LEU cc_start: 0.8583 (mp) cc_final: 0.8356 (mt) REVERT: B 239 ASN cc_start: 0.8612 (m-40) cc_final: 0.8336 (m-40) REVERT: H 109 ASP cc_start: 0.8721 (p0) cc_final: 0.8507 (p0) REVERT: H 221 GLU cc_start: 0.7539 (pm20) cc_final: 0.7149 (pt0) REVERT: R 109 ASN cc_start: 0.4767 (p0) cc_final: 0.4100 (m-40) REVERT: R 127 ASN cc_start: 0.5928 (m-40) cc_final: 0.5721 (m-40) REVERT: R 198 THR cc_start: 0.8398 (t) cc_final: 0.8173 (m) REVERT: R 202 ILE cc_start: 0.8040 (mm) cc_final: 0.7795 (mt) REVERT: R 261 VAL cc_start: 0.7207 (m) cc_final: 0.6815 (p) REVERT: R 280 TYR cc_start: 0.6684 (t80) cc_final: 0.6441 (t80) outliers start: 4 outliers final: 1 residues processed: 247 average time/residue: 0.2345 time to fit residues: 77.0261 Evaluate side-chains 142 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 0.0070 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 255 ASN A 304 GLN B 183 HIS B 220 GLN B 230 ASN H 39 GLN H 143 GLN H 184 GLN R 281 GLN R 345 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8983 Z= 0.182 Angle : 0.527 6.307 12189 Z= 0.277 Chirality : 0.042 0.157 1405 Planarity : 0.004 0.047 1532 Dihedral : 3.721 37.678 1231 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.30 % Allowed : 11.30 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1119 helix: 2.65 (0.27), residues: 377 sheet: 1.47 (0.32), residues: 252 loop : -0.99 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.008 0.001 HIS R 170 PHE 0.024 0.001 PHE R 286 TYR 0.012 0.001 TYR R 275 ARG 0.005 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 0.929 Fit side-chains REVERT: A 24 ARG cc_start: 0.7612 (mtm-85) cc_final: 0.7393 (mtm110) REVERT: A 29 LYS cc_start: 0.7570 (ttmm) cc_final: 0.7245 (ttpt) REVERT: A 195 HIS cc_start: 0.7755 (m-70) cc_final: 0.7230 (t-170) REVERT: A 273 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7676 (mm) REVERT: B 221 THR cc_start: 0.8905 (t) cc_final: 0.8583 (m) REVERT: B 268 ASN cc_start: 0.7882 (t0) cc_final: 0.7574 (t0) REVERT: H 23 SER cc_start: 0.8156 (m) cc_final: 0.7902 (t) REVERT: H 90 ASP cc_start: 0.7952 (m-30) cc_final: 0.7682 (m-30) REVERT: H 221 GLU cc_start: 0.7688 (pm20) cc_final: 0.7403 (pt0) REVERT: R 109 ASN cc_start: 0.4595 (p0) cc_final: 0.4190 (m-40) REVERT: R 112 MET cc_start: 0.5871 (pmm) cc_final: 0.5590 (pmm) REVERT: R 198 THR cc_start: 0.8458 (t) cc_final: 0.8214 (m) REVERT: R 202 ILE cc_start: 0.8108 (mm) cc_final: 0.7887 (mt) REVERT: R 280 TYR cc_start: 0.6773 (t80) cc_final: 0.6518 (t80) REVERT: R 393 LEU cc_start: 0.0346 (OUTLIER) cc_final: -0.0082 (pp) outliers start: 31 outliers final: 16 residues processed: 181 average time/residue: 0.2141 time to fit residues: 53.0180 Evaluate side-chains 154 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 83 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.0040 chunk 100 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8983 Z= 0.154 Angle : 0.495 7.351 12189 Z= 0.257 Chirality : 0.041 0.151 1405 Planarity : 0.003 0.045 1532 Dihedral : 3.726 38.211 1231 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.56 % Allowed : 13.11 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1119 helix: 2.51 (0.27), residues: 386 sheet: 1.47 (0.32), residues: 256 loop : -1.08 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.006 0.001 HIS R 170 PHE 0.011 0.001 PHE R 286 TYR 0.011 0.001 TYR R 275 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7519 (ttmm) cc_final: 0.7251 (ttpt) REVERT: A 195 HIS cc_start: 0.7763 (m-70) cc_final: 0.7157 (t70) REVERT: A 249 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8632 (tt) REVERT: A 252 SER cc_start: 0.8991 (t) cc_final: 0.8695 (m) REVERT: A 273 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7649 (mm) REVERT: B 146 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 221 THR cc_start: 0.8863 (t) cc_final: 0.8568 (m) REVERT: B 268 ASN cc_start: 0.7840 (t0) cc_final: 0.7554 (t0) REVERT: G 15 LEU cc_start: 0.8088 (tt) cc_final: 0.7787 (tp) REVERT: H 23 SER cc_start: 0.8232 (m) cc_final: 0.7967 (t) REVERT: H 90 ASP cc_start: 0.8059 (m-30) cc_final: 0.7797 (m-30) REVERT: H 193 MET cc_start: 0.8287 (ptt) cc_final: 0.8075 (ttp) REVERT: H 221 GLU cc_start: 0.7689 (pm20) cc_final: 0.7469 (pm20) REVERT: R 109 ASN cc_start: 0.4587 (p0) cc_final: 0.4213 (m-40) REVERT: R 112 MET cc_start: 0.5657 (pmm) cc_final: 0.5357 (pmm) REVERT: R 165 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7190 (ttt) REVERT: R 198 THR cc_start: 0.8484 (t) cc_final: 0.8225 (m) REVERT: R 202 ILE cc_start: 0.8172 (mm) cc_final: 0.7958 (mt) REVERT: R 280 TYR cc_start: 0.6796 (t80) cc_final: 0.6542 (t80) REVERT: R 303 ARG cc_start: 0.7464 (mmm-85) cc_final: 0.6828 (tpt170) REVERT: R 393 LEU cc_start: 0.0323 (OUTLIER) cc_final: -0.0062 (pp) outliers start: 24 outliers final: 13 residues processed: 162 average time/residue: 0.2072 time to fit residues: 46.0029 Evaluate side-chains 152 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8983 Z= 0.201 Angle : 0.522 6.823 12189 Z= 0.272 Chirality : 0.042 0.159 1405 Planarity : 0.003 0.042 1532 Dihedral : 3.788 16.981 1229 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.05 % Rotamer: Outliers : 3.84 % Allowed : 14.18 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1119 helix: 2.50 (0.27), residues: 386 sheet: 1.28 (0.32), residues: 259 loop : -1.18 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS R 170 PHE 0.010 0.001 PHE A 196 TYR 0.013 0.001 TYR R 275 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7574 (ttmm) cc_final: 0.7311 (ttpt) REVERT: A 195 HIS cc_start: 0.7774 (m-70) cc_final: 0.7111 (t-170) REVERT: A 249 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8623 (tt) REVERT: A 252 SER cc_start: 0.8975 (t) cc_final: 0.8684 (m) REVERT: A 273 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7687 (mm) REVERT: B 136 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8785 (p) REVERT: B 146 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8089 (mp) REVERT: B 221 THR cc_start: 0.8861 (t) cc_final: 0.8565 (m) REVERT: B 268 ASN cc_start: 0.7802 (t0) cc_final: 0.7537 (t0) REVERT: H 221 GLU cc_start: 0.7757 (pm20) cc_final: 0.7423 (pm20) REVERT: R 132 PHE cc_start: 0.7441 (t80) cc_final: 0.6651 (t80) REVERT: R 165 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7316 (ttt) REVERT: R 202 ILE cc_start: 0.8165 (mm) cc_final: 0.7955 (mt) REVERT: R 280 TYR cc_start: 0.6879 (t80) cc_final: 0.6661 (t80) REVERT: R 303 ARG cc_start: 0.7435 (mmm-85) cc_final: 0.6791 (tpt170) outliers start: 36 outliers final: 22 residues processed: 168 average time/residue: 0.2093 time to fit residues: 48.1635 Evaluate side-chains 161 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS R 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8983 Z= 0.168 Angle : 0.497 6.177 12189 Z= 0.261 Chirality : 0.041 0.212 1405 Planarity : 0.003 0.044 1532 Dihedral : 3.722 16.748 1229 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 2.77 % Allowed : 15.25 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1119 helix: 2.50 (0.27), residues: 386 sheet: 1.19 (0.32), residues: 259 loop : -1.18 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS R 170 PHE 0.011 0.001 PHE A 196 TYR 0.016 0.001 TYR R 341 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7562 (ttmm) cc_final: 0.7296 (ttpt) REVERT: A 195 HIS cc_start: 0.7763 (m-70) cc_final: 0.7118 (t-170) REVERT: A 249 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8641 (tt) REVERT: A 252 SER cc_start: 0.8983 (t) cc_final: 0.8678 (m) REVERT: A 273 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7709 (mm) REVERT: B 146 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7972 (mp) REVERT: B 221 THR cc_start: 0.8820 (t) cc_final: 0.8532 (m) REVERT: B 228 ASP cc_start: 0.8628 (m-30) cc_final: 0.8418 (m-30) REVERT: B 268 ASN cc_start: 0.7790 (t0) cc_final: 0.7546 (t0) REVERT: H 23 SER cc_start: 0.8405 (m) cc_final: 0.8124 (t) REVERT: H 38 ARG cc_start: 0.8561 (ttp-170) cc_final: 0.8155 (ttm170) REVERT: H 221 GLU cc_start: 0.7759 (pm20) cc_final: 0.7439 (pm20) REVERT: R 132 PHE cc_start: 0.7438 (t80) cc_final: 0.6876 (t80) REVERT: R 165 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7309 (ttt) REVERT: R 202 ILE cc_start: 0.8144 (mm) cc_final: 0.7896 (mt) REVERT: R 280 TYR cc_start: 0.6864 (t80) cc_final: 0.6650 (t80) REVERT: R 303 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.6756 (tpt170) outliers start: 26 outliers final: 19 residues processed: 158 average time/residue: 0.2242 time to fit residues: 48.0258 Evaluate side-chains 154 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8983 Z= 0.259 Angle : 0.557 8.120 12189 Z= 0.294 Chirality : 0.043 0.201 1405 Planarity : 0.004 0.042 1532 Dihedral : 4.097 18.983 1229 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 3.52 % Allowed : 14.82 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1119 helix: 2.43 (0.27), residues: 384 sheet: 0.80 (0.31), residues: 267 loop : -1.25 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS R 170 PHE 0.012 0.001 PHE B 234 TYR 0.013 0.001 TYR R 341 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7631 (ttmm) cc_final: 0.7351 (ttpt) REVERT: A 195 HIS cc_start: 0.7768 (m-70) cc_final: 0.7152 (t-170) REVERT: A 249 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8592 (tt) REVERT: A 252 SER cc_start: 0.8998 (t) cc_final: 0.8696 (m) REVERT: A 273 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7724 (mm) REVERT: A 305 CYS cc_start: 0.7823 (t) cc_final: 0.7220 (m) REVERT: B 46 ARG cc_start: 0.7984 (mpt180) cc_final: 0.7716 (mtm-85) REVERT: B 136 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8777 (p) REVERT: B 221 THR cc_start: 0.8849 (t) cc_final: 0.8573 (m) REVERT: H 23 SER cc_start: 0.8414 (m) cc_final: 0.8133 (t) REVERT: H 38 ARG cc_start: 0.8691 (ttp-170) cc_final: 0.8271 (ttm170) REVERT: H 221 GLU cc_start: 0.7906 (pm20) cc_final: 0.7552 (pm20) REVERT: R 127 ASN cc_start: 0.7098 (m-40) cc_final: 0.6651 (m110) REVERT: R 187 LEU cc_start: 0.7277 (tt) cc_final: 0.6666 (mt) REVERT: R 202 ILE cc_start: 0.8195 (mm) cc_final: 0.7971 (mt) REVERT: R 280 TYR cc_start: 0.7042 (t80) cc_final: 0.6795 (t80) REVERT: R 303 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.6590 (tpt170) outliers start: 33 outliers final: 23 residues processed: 158 average time/residue: 0.2265 time to fit residues: 48.2297 Evaluate side-chains 154 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8983 Z= 0.170 Angle : 0.507 6.352 12189 Z= 0.268 Chirality : 0.041 0.196 1405 Planarity : 0.003 0.042 1532 Dihedral : 3.840 17.480 1229 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 3.09 % Allowed : 15.88 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1119 helix: 2.49 (0.27), residues: 385 sheet: 0.80 (0.32), residues: 266 loop : -1.21 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.011 0.001 PHE R 223 TYR 0.014 0.001 TYR R 341 ARG 0.002 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7606 (ttmm) cc_final: 0.7301 (ttpt) REVERT: A 195 HIS cc_start: 0.7766 (m-70) cc_final: 0.7180 (t-170) REVERT: A 249 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8632 (tt) REVERT: A 252 SER cc_start: 0.8992 (t) cc_final: 0.8677 (m) REVERT: A 273 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 305 CYS cc_start: 0.7810 (t) cc_final: 0.7218 (m) REVERT: B 46 ARG cc_start: 0.8016 (mpt180) cc_final: 0.7733 (mtm-85) REVERT: B 221 THR cc_start: 0.8797 (t) cc_final: 0.8540 (m) REVERT: H 23 SER cc_start: 0.8434 (m) cc_final: 0.8174 (t) REVERT: H 38 ARG cc_start: 0.8610 (ttp-170) cc_final: 0.8197 (ttm170) REVERT: H 167 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8942 (tt) REVERT: R 127 ASN cc_start: 0.6890 (m-40) cc_final: 0.6467 (m110) REVERT: R 132 PHE cc_start: 0.7475 (t80) cc_final: 0.6882 (t80) REVERT: R 187 LEU cc_start: 0.7169 (tt) cc_final: 0.6641 (mt) REVERT: R 202 ILE cc_start: 0.8189 (mm) cc_final: 0.7969 (mt) REVERT: R 279 LEU cc_start: 0.7101 (mm) cc_final: 0.6843 (mt) REVERT: R 280 TYR cc_start: 0.6932 (t80) cc_final: 0.6657 (t80) REVERT: R 303 ARG cc_start: 0.7371 (mmm-85) cc_final: 0.6595 (tpt170) outliers start: 29 outliers final: 21 residues processed: 152 average time/residue: 0.2280 time to fit residues: 46.4684 Evaluate side-chains 153 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8983 Z= 0.169 Angle : 0.503 6.295 12189 Z= 0.265 Chirality : 0.041 0.201 1405 Planarity : 0.003 0.043 1532 Dihedral : 3.783 17.459 1229 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 3.30 % Allowed : 16.20 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1119 helix: 2.53 (0.27), residues: 384 sheet: 0.87 (0.32), residues: 260 loop : -1.19 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS R 170 PHE 0.010 0.001 PHE R 223 TYR 0.013 0.001 TYR R 341 ARG 0.007 0.000 ARG R 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.919 Fit side-chains REVERT: A 29 LYS cc_start: 0.7588 (ttmm) cc_final: 0.7283 (ttpt) REVERT: A 195 HIS cc_start: 0.7765 (m-70) cc_final: 0.7149 (t-170) REVERT: A 249 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 252 SER cc_start: 0.8977 (t) cc_final: 0.8672 (m) REVERT: A 273 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7754 (mm) REVERT: A 305 CYS cc_start: 0.7795 (t) cc_final: 0.7210 (m) REVERT: A 313 ARG cc_start: 0.7652 (tpt90) cc_final: 0.7445 (tpt90) REVERT: B 46 ARG cc_start: 0.7968 (mpt180) cc_final: 0.7691 (mtm-85) REVERT: B 136 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8758 (p) REVERT: B 221 THR cc_start: 0.8787 (t) cc_final: 0.8534 (m) REVERT: H 23 SER cc_start: 0.8463 (m) cc_final: 0.8208 (t) REVERT: H 38 ARG cc_start: 0.8600 (ttp-170) cc_final: 0.8186 (ttm170) REVERT: R 127 ASN cc_start: 0.6864 (m-40) cc_final: 0.6453 (m110) REVERT: R 185 CYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5692 (t) REVERT: R 187 LEU cc_start: 0.7096 (tt) cc_final: 0.6597 (mt) REVERT: R 202 ILE cc_start: 0.8190 (mm) cc_final: 0.7969 (mt) REVERT: R 279 LEU cc_start: 0.7096 (mm) cc_final: 0.6791 (mt) REVERT: R 280 TYR cc_start: 0.6896 (t80) cc_final: 0.6617 (t80) REVERT: R 303 ARG cc_start: 0.7389 (mmm-85) cc_final: 0.6575 (tpt170) outliers start: 31 outliers final: 24 residues processed: 147 average time/residue: 0.2331 time to fit residues: 46.0485 Evaluate side-chains 154 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.0030 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8983 Z= 0.160 Angle : 0.501 6.321 12189 Z= 0.264 Chirality : 0.041 0.205 1405 Planarity : 0.003 0.047 1532 Dihedral : 3.743 17.451 1229 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 3.30 % Allowed : 15.78 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1119 helix: 2.55 (0.27), residues: 384 sheet: 0.92 (0.32), residues: 253 loop : -1.21 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS R 170 PHE 0.010 0.001 PHE R 223 TYR 0.013 0.001 TYR R 341 ARG 0.006 0.000 ARG R 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.044 Fit side-chains REVERT: A 29 LYS cc_start: 0.7589 (ttmm) cc_final: 0.7284 (ttpt) REVERT: A 195 HIS cc_start: 0.7770 (m-70) cc_final: 0.7164 (t-170) REVERT: A 198 MET cc_start: 0.8652 (ttm) cc_final: 0.8364 (mtm) REVERT: A 249 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 252 SER cc_start: 0.8977 (t) cc_final: 0.8626 (m) REVERT: A 273 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7741 (mm) REVERT: A 305 CYS cc_start: 0.7797 (t) cc_final: 0.7209 (m) REVERT: B 136 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8763 (p) REVERT: B 221 THR cc_start: 0.8788 (t) cc_final: 0.8538 (m) REVERT: H 23 SER cc_start: 0.8457 (m) cc_final: 0.8201 (t) REVERT: H 38 ARG cc_start: 0.8578 (ttp-170) cc_final: 0.8174 (ttm170) REVERT: R 185 CYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5752 (t) REVERT: R 187 LEU cc_start: 0.6968 (tt) cc_final: 0.6513 (mt) REVERT: R 202 ILE cc_start: 0.8186 (mm) cc_final: 0.7967 (mt) REVERT: R 279 LEU cc_start: 0.7067 (mm) cc_final: 0.6760 (mt) REVERT: R 303 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.6589 (tpt170) outliers start: 31 outliers final: 25 residues processed: 154 average time/residue: 0.2419 time to fit residues: 49.9592 Evaluate side-chains 158 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.0470 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8983 Z= 0.219 Angle : 0.545 7.205 12189 Z= 0.288 Chirality : 0.042 0.211 1405 Planarity : 0.004 0.051 1532 Dihedral : 3.941 17.609 1229 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 3.30 % Allowed : 15.67 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1119 helix: 2.42 (0.27), residues: 384 sheet: 0.77 (0.32), residues: 266 loop : -1.26 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS R 170 PHE 0.011 0.001 PHE A 274 TYR 0.013 0.001 TYR R 341 ARG 0.006 0.000 ARG R 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 1.014 Fit side-chains REVERT: A 29 LYS cc_start: 0.7588 (ttmm) cc_final: 0.7296 (ttpt) REVERT: A 195 HIS cc_start: 0.7764 (m-70) cc_final: 0.7147 (t-170) REVERT: A 198 MET cc_start: 0.8689 (ttm) cc_final: 0.8398 (mtm) REVERT: A 249 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8633 (tt) REVERT: A 252 SER cc_start: 0.9000 (t) cc_final: 0.8669 (m) REVERT: A 273 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7764 (mm) REVERT: A 305 CYS cc_start: 0.7820 (t) cc_final: 0.7264 (m) REVERT: B 46 ARG cc_start: 0.7999 (mpt180) cc_final: 0.7735 (mtm-85) REVERT: B 136 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8779 (p) REVERT: B 221 THR cc_start: 0.8817 (t) cc_final: 0.8557 (m) REVERT: H 23 SER cc_start: 0.8461 (m) cc_final: 0.8203 (t) REVERT: H 38 ARG cc_start: 0.8652 (ttp-170) cc_final: 0.8233 (ttm170) REVERT: R 127 ASN cc_start: 0.7149 (m-40) cc_final: 0.6730 (m110) REVERT: R 185 CYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5771 (t) REVERT: R 187 LEU cc_start: 0.7073 (tt) cc_final: 0.6557 (mt) REVERT: R 202 ILE cc_start: 0.8171 (mm) cc_final: 0.7894 (mt) REVERT: R 279 LEU cc_start: 0.7098 (mm) cc_final: 0.6812 (mt) REVERT: R 303 ARG cc_start: 0.7401 (mmm-85) cc_final: 0.6574 (tpt170) outliers start: 31 outliers final: 26 residues processed: 143 average time/residue: 0.2291 time to fit residues: 44.1392 Evaluate side-chains 152 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108128 restraints weight = 11020.156| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.98 r_work: 0.3058 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8983 Z= 0.228 Angle : 0.547 7.344 12189 Z= 0.289 Chirality : 0.042 0.180 1405 Planarity : 0.004 0.050 1532 Dihedral : 4.018 17.830 1229 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 3.20 % Allowed : 15.88 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1119 helix: 2.38 (0.27), residues: 384 sheet: 0.70 (0.32), residues: 265 loop : -1.32 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS R 170 PHE 0.011 0.001 PHE R 223 TYR 0.015 0.001 TYR R 280 ARG 0.006 0.000 ARG R 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2297.35 seconds wall clock time: 41 minutes 32.79 seconds (2492.79 seconds total)